


Two Birds and a Stone

by SherlockedinStohess



Category: Star Trek, Star Trek: Alternate Original Series (Movies)
Genre: F/M, Friendship, Khan's a BAMF, Khan's fucking awesome, More than one superhuman, New Character - Freeform, Non-Canon Relationship, Violence, seriously though
Language: English
Status: In-Progress
Published: 2013-06-06
Updated: 2013-07-10
Packaged: 2017-12-14 02:30:25
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 2
Words: 3,294
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/831686
Author URL: https://archiveofourown.org/users/SherlockedinStohess/pseuds/SherlockedinStohess
Summary: <blockquote class="userstuff">
              <p>Two years after the crash of The Vengeance, Khan's sentence has been changed. Woken from his sleep and with an electrical chip in his head, ex-terrorist John Harrison will be sent aboard the Enterprise to work as a crewman. Slowly, the rest of the crew start to trust him and he forms a strange friendships with Captain Kirk. But will all of that be destroyed when one of Khan's family wakes up?</p>
            </blockquote>





	1. Chapter I

**Author's Note:**

> After seeing _Star Trek: Into Darkness_ with the lovely Benedict Cumberbatch for the four times in a week, I decided I would try to attempt a Star Trek fanfic. I've never been a huge fan, and after sitting through all the episodes of every season of _Star Trek: Deep Space Nine_ in one summer with my grandma, I didn't like it much. A thank you to Benedict for changing my mind with his incredible voice and villainy sexiness.

**Year 2003.21.05**

* * *

Deep, deep in the pits of the earth it cried. Dark, dark down in the center it screamed. The flashing lights burned its eyes, set the fire in its veins ablaze as it writhed and yelled and kicked and shrieked. Sharp pin pricks turned to a thousand knives, stabbing and gouging all over its skin as it pleaded for the pain to stop.

"Shhh, it's all right my dear. It will be over soon. Then you will be complete," the shadows whispered, always whispered.

"I just want it to stop," it whimpered. "Please, just make it stop."

"Now, you know I can't do that Myra." It flinched at the sound of that name; it wasn't that name anymore, why did they keep calling it that?

With a final breath, its heart stopped beating and a searing pain, a blinding white light, enveloped its mind. Brightness turned to dull gray, pain turned to nothing and hell turned to heaven.

"The augmentation is complete."

* * *

**Year 2261.06.11**

* * *

"He did what?!" Kirk yelled. McCoy smirked at his friends' anger.

"It's Spock, Jim, of course he's going to do this. Don't you remember last time?" Kirk turned on his old friend, a different kind of anger, mixed with sadness, in his eyes. Leonard realized his mistake too late.

"Yeah, the last time, right before Pike died! Thank you Bones, thank you very much, that's just what I needed right now!" he fumed. "You know, why can't he just rein in his stupid Vulcan-ness and just do what he should for once? The Admiral doesn't need _another_ report detailing how I broke the rules over some stupid, uncivilized species seeing our ship. It's not like we're going to see them again anyway."

"Jim, I'm sorry. But honestly, you keep expecting him to budge when he obviously isn't going to, at least not as soon as you think. He's a Vulcan, and moreover, he's Spock. It's only logical to assume he won't change," he teased, raising a mocking eyebrow. Jim's mouth twitched upward, and before long, they both burst into loud peals of laughter.

"Oh God, oh God," Jim cried as he clutched his stomach. They slapped their hands on the desk, tears threatening to spill over as the hysteria, the stress and the anger all came out in that one laugh.

"I'm glad you find the childish mockery of your peers soothing Captain, but right now we have more urgent matters to attend to." Both men turned to see a Vulcan with neatly trimmed hair, slanted eyebrows and a blue Star Fleet shirt staring at them in what could be derision. Or he was just constipated.

"Spock…uh…we were just, uh…"

"There is no time for excuses or apologies Captain. Admiral Josen is waiting for you on the bridge." Spock turned, back ramrod straight, and proceeded down the hallway, leaving a breathless Kirk and McCoy to catch up.

With everyone in formal position, Lieutenant Uhura connected with the hailing, and the rounded, aged face of Admiral Josen appeared on the screen.

"Hello sir, what can I do for you today?" Kirk asked, hoping to whatever power existed that this had nothing to do with his and Spock's most recent reports.

Later he would wish it had been just that.

"I wish I came with easier tidings son, but I'm afraid I have some…shocking news."

"Is this about the mission Planet J319? Because sir, while it was a violation of our orders for this voyage, I can assure you—"

"No, it's not about that. I doubt I could change your ways if Admiral Pike couldn't, and I understand why you did what you did. This times, it slides, in the face of the bigger issue."

"Bigger issue?" Kirk questioned, shooting a nervous glance to Bones and Spock, who returned it; well, Spock as best as a Vulcan could.

"Kirk, as you know, the trial for Khan Noonien Singh was held five months after the incident with Admiral Markus. It has been two year since then, and Khan's sentence has changed. Since you are directly involved, both now and then, it was necessary to inform you."

"Inform me of what?" Jim snapped, a rare edge to his voice. Every single person in the room was transfixed on the screen.

"After some experimentation, the depth of which I will not say, it has been determined that Khan will be more useful outside of his tube, rather than within it."

"You're not actually considering letting that maniac out are you?" McCoy bellowed. "He killed two Star Fleet Admirals, over two-hundred people and destroyed almost all of the Star Fleet head quarters! Not to mention he caused the devastation in San Francisco!"

"I am well aware of the damage son," Josen replied, fixing an icy stare that had no effect whatsoever on the good doctor. "Right now we need all the hands we can get. Since your crew, Kirk, is the only group of people with any experience in dealing with this man, he will be sent on a shuttle to you in two weeks time. He has been informed that if he does anything outside of the orders he receives from you, Captain, he will be detained and put back in his tube."

"Sir, all due respect, but how will this help? It is quite apparent that Khan can and will find a way around that rule, just as he did with Admiral Markus. I do not feel it would be logical or safe for this crew to be around this man," Spock interjected.

"That's where the experiments come in." the Admiral pulled out a folder of papers and flipped through several before speaking again. "Recent developments in technology have allowed us to create a behavior modification device, or a BMD. This is what our doctors implanted in his brain several weeks ago, and they have proven beyond a doubt that it works. I will have more info for you on this when he arrives, Captain, as it is classified." Not another word was spoken for several minutes, the emotions floating in the air too heavy and thick for verbal expression.

Josen looked around the room; angry McCoy, fearful Chekov, shocked Uhura and contemplative Spock.

The Captain, however, was a whole other story.

"All right," he agreed, earning him yells from all over the bridge.

"Thank you. That was a lot easier than I thought it would be. I will send you the information you'll need for his arrival." And with that, the transmission cut out.

Silence filled the room.

As far as Jim was concerned, his brain had been utterly fried. First Spock, then making repairs to the ship, then filling out the Captain's Log, then filing paperwork and now _this_? This was turning out to be a very bad day. He might as well comply, if only to get it over with. He had been in enough deep shit, and knew a dive right back into it when he saw one. That hadn't been a request, it had been an order, and frankly, he just wanted sleep and alcohol at the moment.

"Jim, how could you allow that monster onto the _Enterprise_?" Bones hissed once he was close enough.

"I agree, Captain, this decision is a foolhardy one at best," Spock added. Jim held up his hands for a moment of silence.

"Did it ever occur to either of you that now he can get what he deserves?" Two shocked and confused faces stared at him. "Look, I've read about these 'BMDs' before; they send electrical impulses or something through the brain when a trigger is pressed. If Khan even so much as looks at someone the wrong way, or I feel that anyone on this ship is marginally threatened by him, I can take that bastard down with a click of a button! Sure, it's not very humane, but he did kill and hurt people I, _we_ , cared about. This is the perfect chance to get back, and there's no way in hell I'm passing it up." At this point, Bones was grinning from ear to ear, a bit of evil mischief in his eyes.

"Captain…" Kirk and McCoy both groaned aloud; they knew that 'I-have-an-obscenely-logical-objection' tone of voice. "While I do agree that Khan should be punished, I am not sure this is the proper way to go about it. He deserves to live his life in a maximum security prison or frozen with the rest of his people, but I fear that this opportunity may cause you to lose sight of your role as Captain. This is petty revenge, and if it impacted the crew in any way, I know that none of us would feel justice was served as it was meant."

Two pairs of stoic eyes gazed at the Vulcan. Of course, he didn't twitch or avert his gaze like a normal human; he just raised an eyebrow in that annoying way of his. For once, it wasn't him who had locked off his emotions, but the Captain.

"Too bad," Kirk said quickly and dashed to his office, leaving his Commander and Chief Doctor in the dust.

There was no way he would let this opportunity slide by. Oh no, no, no, he would take full advantage.

After all, revenge is a dish best served burning hot.


	2. Chapter 2

**Summary for the Chapter:**

> The crew of the Enterprise get ready to meet the man who nearly destroyed their lives. Kirk isn't too happy about it.

**Notes for the Chapter:**

> I am so terribly sorry about the huge delay my ducks! Like I said last chapter, the only time I have to work on this is basically on the weekends. And though I may be a huge nerd, I do have somewhat of a life, so that time is cut even shorter. Hopefully you will like this chapter and decide to forgive me *grovels* And thanks to all who reviewed!

Fingers tapped impatiently against the arm of Jim's chair. Every nerve was on edge, every thought consumed with anxiety over the day's swiftly approaching plans. The arrival of their special _guest_ loomed on the horizon. Only now, Jim had the endless, and in this case _not_ comforting, horizon of space to look upon.

"Keptin, ve vill be nearing zhe planet's atmosphere in approximately terteen minutes," Chekov announced from his spot near the shuttle bridge, tapping away on his PADD. Every spine went rigid, every heart skipped a beat, as everyone drew in a sharp breath. By now all crew members knew what was coming, a mixture of fear, anticipation, curiosity and wariness filling the room. The only one who remained calm, at least on the outside, was Commander Spock, sitting stiffly next to his captain.

"Okay," Jim replied through gritted teeth. Everybody knew he was on edge. The very man who had been the cause of his death, even indirectly, and who was also the one who saved his life, was about to become a member of their crew. He had no say; this, sadly, was a case where the Admirals pulled rank on him and demanded he follow an order. This order, especially, would not be trifled with. One of the few rules he couldn't, and wouldn't, mess with.

For the past several days, he had been waiting. No matter where he was, whether it was his chambers or the bridge or the bar, Khan constantly invaded his mind. The very man who had taken so much from him would now be under his command. At first he had been excited, what with the man's new 'chip' in his brain that Jim had control over.

But then he remember when they had captured Harrison —Khan, Singh, whatever—that they had only done so because that had been what the super human wanted at the time. Who was to say that this wasn't the exact same situation?

Khan could not be trusted, everyone knew that. Though they had covered it up, StarFleet had recognized their mistake and their ignorance in the actions of Admiral Markus. It had been kept quiet, and soon things were sorted out. Yet, of course, the idea of a militarized StarFleet was never very far off, and now that Markus had inadvertently started a movement, despite the tragic ending of his determination, the idea had spread. Ideas are like seeds; all they ever need to grow is for someone to spread them.

So the science section of HQ had secured Khan and his crew, reverting back to their tests and experiments, though there was proof that this time, the experiments were far more humane than those that Markus had submitted Khan to.

Jim hadn't forgiven the guy; far from it. He wanted to see him burn as much as anybody else; he had killed Pike for God's sake. The man who had made him (or pushed him depending on how you look at it) to be the man and Captain he was today. But everyone had a right to a fair trial and Jim was certain the court case for Khan was just a show, and now his coming to the Enterprise the test. They wanted to see how their technology worked, and how useful the super human could be under their control.

He might not have forgiven or forgotten, but he was capable of _some_ compassion for the bastard. Or any other bastards for that matter.

"Captain?" Kirk looked to see most of his bridge crew staring at him, all of them cramped into the small shuttle. He lifted an eyebrow in confusion and glanced at Spock, eyes trained on him worriedly.

"Huh?" he asked stupidly.

"We have entered the atmosphere and are preparing to land. Awaiting your orders for action."

Oh.

"Contact the awaiting Admirals and let them know we are prepared for all arrangements, as well as for our…guest." He spoke with as much seriousness as possible, but this was his crew. They could tell, see, the fear curling inside of him, the anxiousness roiling beneath the surface. Because they all had it as well. But now was not a time for fear, and if their Captain and Commander hid it, then they would too.

The shuttle shook a bit as the turbulence from entering the lower levels of the atmosphere passed over them, and soon they were in the last few minutes of smooth sailing before they finally landed on solid earth. Then the metal of the ship groaned and lurched.

"What the hell was that?" he yelled, gripping the arm rests of his chair tightly.

"There seems to be a problem with engine two sir, we're fixing it." Kirk looked at Chekov and Scotty, who had been sitting side by side conversing about some equation. They nodded and unhooked the safety belts, hurrying to the front of the large shuttle to help.

"This is just what we need," Bones growled from behind him. "Going off to meet a maniac who's tried to kill us, sure, of course our shuttle needs to crash. Stupid god damn ship, stupid god dam space…"

Despite the situation, Jim couldn't help but chuckle at Bone's ability to curse out anything, anywhere.

He was ripped out his musing when another strong jolt made him lurch forward, hurting his stomach as the seat belt kept him in the seat.

"I really hate these things," he muttered before ripping it off and running to the front. He ignored Spock's surprised shout of 'Captain!' and slapped a hand of Scotty's shoulder as he reached the control station. "What's going on? Why are we failing?"

"One o' the smaller turbines fell off an' is stuck between the rotors of the main engine, sir. We can't get ou' there to fix it 'til we've landed."

"But how can we land with a busted engine?" The Scot looked at him, pained.

"Zat's zhe problem sir. Ve can't vithout seriously damaging zhe ship and its passengers," Pavel chimed, for once that puppy dog look gone. Instead, it was replaced with something Kirk hated to see in such a young face.

Fear.

"Don't worry, we've survived a lot worse than this, Pavel. We'll be fine." The Russian seemed to cheer up a bit at the rare use of his first name (since it was considered inappropriate in professional settings) and turned to continue speaking with one of the flight attendants, spewing evacuation instructions.

But they all knew that a shuttle didn't have very many safe or usable evacuation drills. Hell, the reason for the damn shuttle _was_ evacuation. There was only one layer, and they were on it now.

"Please keep your seat belts fastened and prepare for crash landing," a mechanical voice called over the intercoms.

"That includes you Captain, and your crewmates," the pilot cried, straining to the control the wonton ship. With a mini-showdown, they glared at each other until another shudder of the ship made Kirk herd Scotty and Chekov out to their seats.

"Everybody hold—" Jim never finished the sentence, because at that moment, the bottom of the shuttle nicked a rocky hilltop two miles from the landing station. The loud snarl of rock hitting metal was unmistakable. The Captain flew across the cabin, smashing into the wall as everybody started yelling in fear. The walls rocked and the windows cracked as the rough landing inevitably took its toll on the small ship, and the passengers.

Finally, the dust cleared and eyes met, panic and fright melting away when the crew realized they had managed to stay relatively unscathed. Spock's worried gaze met Kirk's, and a small, relieved smile turned up the corner of the Vulcan's lips when all Jim did was get up and stretch, instead of keeling over from the harsh impact hit he took. After several minutes of organizing, they carefully disembarked. The worst injury was a dislocated wrist, something Bones easily (and quite angrily, Jim might say) fixed before wrapping the girl's arm in a torn piece of cloth to keep it in place. She nodded a teary thanks.

"Well, that could have gone a lot better, but hey, at least we're here." Several heads turned to look at him dryly, annoyed by the optimism.

"And by here, do you mean two miles away from the blasted station we were _supposed_ to land at?" McCoy interjected.

"Precisely." Jim replied with a sickeningly sweet smile. "The meds will be here any second, so don't worry. We'll be fine. He clapped a hand on his old friend's shoulder, who just walked away grumbling, pulling out his on-hand medical supplies. It was in times like this that Jim almost felt bad for Leonard, for having to put up with all his crap. Almost.

"Captain, they need help gathering the scattered materials for the wreckage crew to examine," Scotty called.

"Right," he breathed. "I'll take this route." People, or those not injured, started to spread out, combing through the bushes for the leftovers of their ship. Mostly for something to do while the ambulances took their sweet time.

Jim had been looking around a group of ferns when light broke through the sparse tree coverage. He blinked before smiling softly. Sunset. It had been one of the things he missed the most about Earth; there were no sunsets, or sunrises, in space.

He took a step forward without thinking, only to find the rock below his foot crumbling and his world starting to tilt. With a shout, he fell, reaching toward nothing as his hand grasped at air. He closed his eyes, waiting for the inevitable impact of his head meeting solid ground. To think, he had survived an attack from Romulans from the future, a volatile volcano, getting the crap beaten out of him by a mad Vulcan and literally getting killed by a psychotic superhuman. And here he was, meeting his end by falling off a cliff.

Suddenly the falling stopped, but the pain was in his arm, not his head. Cracking one eye open, he saw he was still about forty feet from the ground, just hanging over the side of the crag. With wide, incredulous eyes he looked up into a pair of fierce, light blue orbs and a cold smirk. A deep, resonating baritone filled his ears as his mouth fell open in shock.

"Hello _Captain_."

**Notes for the Chapter:**

> So, a bit longer than last chapter. The next one I will try to have out next week(end?), but I really don't know since my schedule is so hectic. Thank you to all who review and have reviewed, I appreciate it so much.

**Author's Note:**

> I'll try to make next chapter longer. Hope you liked!


End file.
